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X-ray Crystal Structure of a Chemically Synthesized Ubiquitin with a Cubic Space Group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YIW PDB entry 1YIW, CHAIN B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.75 298 by mixing 2 ul of ubiquitin solution (20 mg/ml) and 0.5 ul of crystallization buffer solution. The crystallization buffer was prepared by mixing 3ml of HEPES buffer (0.1M), 3ml of poly(ethylene glycol) 3350 (25%, w/v), and 0.2ml of 1M cadmium acetate, pH 7.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.82 56.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.059 α = 90 b = 105.059 β = 90 c = 105.059 γ = 90
Symmetry Space Group P 43 3 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 210 MIRRORS 2004-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0000 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3.3 30 99.6 0.072 23.9 11.9 3300
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.3 3.42 100 0.66 3.2 12.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1YIW, CHAIN B 3.3 20 2958 293 99.75 0.25 0.24617 0.24149 0.2522 0.28563 0.2908 RANDOM 85
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.629 r_dihedral_angle_3_deg 17.007 r_dihedral_angle_4_deg 9.22 r_dihedral_angle_1_deg 6.63 r_angle_refined_deg 1.313 r_angle_other_deg 0.715 r_symmetry_vdw_refined 0.268 r_metal_ion_refined 0.257 r_nbd_refined 0.24 r_symmetry_vdw_other 0.221
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.629 r_dihedral_angle_3_deg 17.007 r_dihedral_angle_4_deg 9.22 r_dihedral_angle_1_deg 6.63 r_angle_refined_deg 1.313 r_angle_other_deg 0.715 r_symmetry_vdw_refined 0.268 r_metal_ion_refined 0.257 r_nbd_refined 0.24 r_symmetry_vdw_other 0.221 r_nbd_other 0.188 r_symmetry_hbond_refined 0.188 r_xyhbond_nbd_refined 0.158 r_nbtor_other 0.08 r_chiral_restr 0.067 r_bond_refined_d 0.012 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1164 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing